Added the new runtime option MEKE_ADVECTION_BUG and corrected a bug in the
calculation of the vertically integrated transport for the advection of the
MEKE field when MEKE_ADVECTION_FACTOR > 0.  The default is to fix the bug, so
answers can change in some cases by default, and in those cases there are
changes to the MOM_parameter_doc files, but this option is not widely used and
there are no answer changes in the MOM6-examples test suite.  This PR addresses
MOM6 issue mom-ocean#1465, which can be closed once this PR is merged into dev/gfdl.

  Added a runtime flag, BAROTROPIC_TIDAL_SAL_BUG, to fix a sign error in the
tidal self-attraction and loading anomalies in the barotropic solver when tides
are enabled.  The default is to keep the previous bug so that answers do not
change, but this default will be changed after solutions have been corrected.
This commit partly addresses MOM6 issue mom-ocean#1496, but it should only be considered
to be properly handled once the default has been changed to avoid this bug.
This commit will change the MOM_parameter_doc files in cases where this bug
matters, but by default all answers are bitwise identical.

…ugfix

(+*)Fix MEKE advection bug

+Add BAROTROPIC_TIDAL_SAL_BUG to fix a tide bug

* first draft API based on Luyu's code
* fixed various errors
* Code for particles in MOM.F90
* moved particles_run into dynamics step
* added particles_end
* Fixed particle time
* Fixed some documentation
* Further documentation edits
* converted pointers to allocatables in particles_gridded
* Remove trailing space
* Further doxygen tweaks
* another trailing space
* removed set_time

Co-authored-by: Cory Spencer Jones <spencerjones@login4.cluster>

Esmg docs

FMS mpp domain creation is done in the `clone_MD_to_d2D` function, and
currently an IO domain is always created within the MPP domain.

This has caused problems with single-PE runs in FMS1, where the
`write_field` logic was not able to reach the part which removes halo
data if an IO domain was present, and halo data was being written to the
restart files.

This issue arose when `PARALLEL_RESTARTFILES` was set to `True` for
single-PE tests.

This does not appear to be a problem with FMS2, and no action is needed
by the FMS team.

* Revert "Implement changes suggested by @Hallberg-NOAA"

This reverts commit 8f4af3d.

* Revert "*Corrected the clock as seen by diabatic processes"

This reverts commit bc6c6e6.

* Revert "*Use rho_ref in finite volume PGF density calcs"

This reverts commit 48e90d0.

* Update of MOM6 code to allow SPEAR to reproduce previous answers.

Updates MOM code to dev/gfdl as of 2/7/2019 (6dd6f52) and reverts 3 answer changing modifications.
Update produced by

git revert 8f4af3d
git add src/tracer/MOM_neutral_diffusion.F90
git revert --continue
git revert bc6c6e6
git add src/core/MOM.F90
git revert --continue
git revert 48e90d0
git add src/equation_of_state/MOM_EOS.F90
git revert --continue

Some conflict resolution was needed.

* Optional use of differing restoring piston velocities for temp and salt

* Correction to ePBL code to mitigate blowup.

Also "corrects" some spelling differences in variables (MStar vs mstar)

* add MJHarrison-GFDL salt_flux_add_fix to SPEAR codeset

from
https://github.com/MJHarrison-GFDL/MOM6/compare/salt_flux_add_fix

* Added ability to change remapping scheme.

Added call for parameter REMAPPING_SCHEME to allow changes to be made.
Previously was hardwired to PLM.

Call for MOM_grid_int was issing a global_indexing=F argument

Tests indicated that oda clocks were being called out of order and
crashing the test, so I commented them out.

* Removed timers, Changes name for REMAPPING_SCHEME parameter

Changes REMAPPING_SCHEME to ODA_REMAPPING_SCHEME
Removed timers that were causing blowups

* Adds documentation for ODA_remapping_scheme

Changes second argument to get_param calls to the module name.

Co-authored-by: Matthew Harrison <Matthew.Harrison@noaa.gov>

NOTE: Initial submission included 4 parameters.
`PARALLEL_RESTARTFILES` was dropped after an issue was detected.

Full commit log history below.

* +*Change defaults for 4 parameters to better values

  Updated the defaults of 4 run-time parameters (INTERNAL_WAVE_SPEED_BETTER_EST,
PARALLEL_RESTARTFILES, EPBL_MLD_BISECTION, and BBL_USE_EOS) to more appropriate
values.  In each case, the previous default was simply the older setting, and
not the better recommendation.  It also adds logic determining whether
SIMPLE_TKE_TO_KD does anything, and only log its setting if it does.  These
default changes were discussed by the MOM6 consortium as a whole in June, 2021
and were widely agreed to. In addition this commit removes the old obsoleted
runtime parameter ORIG_MLD_ITERATION, and obsoletes the runtime parameter
LARGE_FILE_SUPPORT, and it adds comments describing several real variables and
their units.  Because this changes several default values, it will change
answers unless these parameters are explicitly set in the MOM_input files.
However, because MOM6-examples PR mom-ocean#344 does set these values to their old
defaults where they are used, no answers are changed in the MOM6-examples
regression suite, although there are changes to the MOM_parameter_doc files.

* +Reverted default for PARALLEL_RESTARTFILES

  Reverted the default for PARALLEL_RESTARTFILES to False because the TC restart
testing was having problems with this set to True.  This is surprising because
PARALLEL_RESTARTFILES = True has been used in production runs for many years now
without any indication that MOM6 fails to reproduce across restarts in this
mode, so this could be an issue with the TC testing.  In the mean time,
reverting this default will allow the other changes to be accepted while this
curious behavior is explored separately.  Several comments related to
PARALLEL_RESTARTFILES were also updated for consistency. All answers are bitwise
identical.

Add the new runtime parameter FATAL_INCONSISTENT_RESTART_TIME, which if true
causes the model to compare the restart time read from a restart file with any
value provided as a time_in to MOM_initialize_state and issue a fatal error if
they differ.  In ocean-only mode, this input time is read from a ocean_solo.res
file, following FMS behavior.  The default value simply uses the specified time,
replicating the previous behavior.  If set to true, this would prevent a problem
with the time-history that recently occurred in a series of high-resolution runs
that were shared between several groups, where the nominal times were repeated.
All answers are bitwise identical, but many MOM_parameter_doc files have a new
entry.

* +(*)Fix bug when RES_SCALE_MEKE_VISC = True

  Fix a bug that can lead to segmentation faults when RES_SCALE_MEKE_VISC is
true, as noted in MOM6 issue mom-ocean#1464, and add better error handling to detect
related problems.  The refactoring that is a part of this may also avoid some
problems with optimized code even when RES_SCALE_MEKE_VISC it false, as
described in MOM6 issue mom-ocean#1463.  In addition, logic was added so that the value
of RES_SCALE_MEKE_VISC is only logged if USE_MEKE is true.  All answers are
bitwise identical in cases that worked, including the MOM6-examples test suite,
but there are some changes in the MOM_parameter_doc files, due to an irrelevant
parameter no longer being logged.

* (*)Initialize CS%res_scale_MEKE

  Initialize the logical element res_scale_MEKE in the hor_visc_CS even if
there is no Laplacian viscosity, so that a self-consistency test does not use an
initialized value.  Also improved some comments.  All answers are bitwise
identical for all cases that successfully ran before, including in all cases in
the MOM6-examples test suite.

  Made 37 optional arguments that are always present in calls into non-optional
arguments to routines in the src/core directory.  Many of these are pointer
arguments related to things like open boundary conditions, so if these types are
not to be used, they are simply not allocated.  In several cases, this required
the order of the arguments to be shifted around, but the various types of the
arguments should prevent the model from compiling if the calls (e.g., in
user-modified code that is not in the github repository) are not changed
equivalently.  Also eliminated 3 internal arguments in MOM_barotropic.F90 that
are always hard-coded to the same values (the maximize argument to
BT_cont_to_face_areas()) or are never used (the guess arguments to uhbt_to_ubt()
and vhbt_to_vbt()), along with the code that they would exercise.  All answers
and output are bitwise identical.

  Refactored solo_driver/MOM_driver.F90 to move logically self-contained blocks
of code into separate subroutines within this file to improve the readability of
the code and to reduce the number of global variables.  This started out as an
exercise to explore the use of the F2008 block / end block construct to reduce
the scope of variables, but the code ended up being cleaner just using
traditional subroutines contained in this file.  All answers are bitwise
identical and all output files are unaltered.

+Make 37 optional arguments in src/core mandatory

Main to dev

  Made 44 previously optional just_read_params arguments into mandatory
arguments and renamed them just_read to avoid duplicated variables.  This change
should be minimally disruptive, as these optional arguments were always being
provided.  Some argument documentation blocks were also reformatted or the
comments in them were corrected.  All answers are bitwise identical, but some
arguments have changed.

  Cleaned up 27 falsely optional or unused arguments in the vertical
parameterization code, and related changes.  This includes:
 - Eliminating the symmetrize arguments to set_viscous_BBL and set_viscous_ML,
   which are now effectively always true.
 - Making the Waves and OBC pointer arguments mandatory in several routines
   where they were always being supplied.  These are pointers, so the test of
   whether they should be used can be based on whether they are associated.
 - Adding error messages about unassociated Waves types that would be used.
 - Eliminating the unused Waves argument to KPP_init.
 - Eliminating unused arguments that energetic_PBL inherited from the bulk mixed
   layer code, and simplified some disabled debugging code.
 - Making the optics argument to opacity_end mandatory.
 - Making the h argument to get_Langmuir_Number mandatory and rearranged the
   arguments to this routine to put the optional arguments last, following the
   practice elsewhere in the MOM6 code.  Also standardized the case of several
   variables in the MOM_wave_interface.F90 code to facilitate searches.
 - Eliminating the unused US argument to CoriolisStokes.
All answers are bitwise identical, and no output is changed.

This patch uses the FMS2 `file_exists` function when using the FMS2
infra.  Previously, the FMS1 version of this function was being used.

This patch also removes the `mpp_domain` and `no_domain` arguments from
the direct `file_exist` calls, which were not used by any known MOM6
configurations.  (Nor would we expect them to be, since explicit
references to FMS should not exist outside of the infra layer.)

Since FMS2 does not use these arguments, their removal also creates a
more meaningful interface between the two frameworks.

Motivation:

An issue with the FMS1 `file_exists` under the FMS2 infra was discovered
in the UFS model on Hera.  It was only reproducible in submitted jobs,
and not for interactive jobs, and only with the GCC 9.2 compiler.
(Other GCC versions were not tested.)

One potential explanation is that it is related to the `save` attribute
of the domain pointer, `d_ptr`.  In the case above, `d_ptr` pointed to
the MOM input domain for the failed cases.  For the other working
cases, `d_ptr` pointed to a `NULL()` value and behavior was normal.

It is possible that `d_ptr` is inconsisently updated when FMS1 and FMS2
IO operations are used together, which should probably be considered
undefined behavior.

  Eliminated the unused optional OBC argument to write_energy() and several
unused optional arguments to wave_speed() and wave_speeds() that are set instead
via arguments to wave_speed_init() that store these values in a wave_speed_CS
type.  Also made the optional row_scale argument to tridiag_det() and the
tracer_CSp argument to write_energy() that were always present in calls into
mandatory arguments.  All answers are bitwise identical, and solutions do not
change.

FMS1: Don't create IO domains for single-PE domain

  Modified create_file to always specify that the threading will be for a single
PE to do the writing to a single file if there is only a single ocean PE, to
avoid some incorrect behavior inside of the FMS IO modules.  This can fix
restart problems in some single-processor cases with an inconsistent setting of
the optional threading argument, but in all cases that ran correctly before, all
answers are bitwise identical.

  Cleaned up 13 falsely optional or unused arguments in the horizontal
parameterization code, and related changes.  This includes:
- Made the previously optional OBC pointer arguments that were always being used
  in calls to 3 routines in MOM_lateral_mixing_coeffs.F90 into mandatory
  arguments.  Because these are pointers, the deciding factor of whether to use
  them is really whether they are associated.
- Made an internal optional argument that was always being used mandatory in 2
  routines in MOM_internal_tides.F90.
- Made 2 internal optional arguments that were always being used mandatory in
  thickness_diffuse_full().
- Eliminated the unused deta_tidal_deta argument to calc_tidal_forcing() and
  made the m_to_Z argument to the same routine mandatory.  The former value is
  instead obtained by a call to tidal_sensitivity.
- Eliminated 3 unused arguments and made an optional argument that was always
  used mandatory for find_deficit_ratios() in MOM_regularize_layers.F90.

This patch modifies the `cpu_clock_id` interface so that the
`synchro_flag` argument is converted into a platform-agnostic logical
flag.

The current implementation requires the synchronization flag to be
defined using FMS norms (zero-bit) and also would force users to follow
FMS predefined flags for other values.

This patch changes the sync flag to a logical, and modifies the default
flag to enable synced clocks (based on `clock_flag_default`).

`synchro_flag` is also renamed to `sync` for simplicity.

Use FMS2 `file_exists`, remove domain args

cpu_clock_id: synchro_flag arg changed to logical

* Eliminate GET_ALL_PARAMS in hor_visc_init

  Added do_not_log arguments to get_param calls in MOM_hor_visc.F90 that are
only used conditionally, and eliminated the unlogged GET_ALL_PARAMS runtime
parameter and get_all variable in hor_visc_init().  By design, all logging of
parameters after this commit is identical to before, even for variables that are
inactive and therefore should not be logged.  In several places, there were some
problems, mostly with the GME code, that have been noted in comments marked with
'###'.  Also cleaned up the code alignment and eliminated unneeded temporary
variables in a few places in hor_visc().  All solutions are bitwise identical,
and no output is changed.

* Restore temporary variables

  Undid changes that eliminated temporary variables to facilitate performance
profiling, and restored the "Knuth" convention about the placement of the line
breaks relative to "+" in these expressions.  Nothing changes.

This adds four new diagnostics building on the wind stress acceleration diagnostics du_dt_str, dv_dt_str (from mom-ocean#1437)
- their thickness-weighted versions: h_du_dt_str, h_dv_dt_str (completing the set of diags from 3D thickness x momentum diagnostics mom-ocean#1398)
- their viscous remnant fraction: du_dt_str_visc_rem, dv_dt_str_visc_rem (completing the set of diags from Visc_rem_[uv] multiplied momentum budget diagnostics ocean-eddy-cpt#10)

Nora did some quick tests with the CPT NeverWorld2 setup, which confirm that online and offline multiplication by 1) h or 2) visc_rem_[uv] coincide (up to 1) interpolation error and 2) numerical noise, respectively), and illustrated this beautifully with some figures that accompanied the first of the three commits that were squashed into one.

  Cleaned up 26 falsely optional or unused arguments in the vertical
diffusivity code, and related changes.  Several descriptive comments were
also corrected, including the correction of the units of 10 variables related
to CVMix_KPP.  This commit includes:
 - Made the Kd_int arguments to set_diffusivity() and 3 subsidiary routines
   mandatory and reordered the arguments so that the non-optional arguments
   come before the grid types
 - Made the halo_TS and double_diffuse arguments to set_diffusivity_init()
   mandatory.
 - Made the Time argument to ALE_sponge() mandatory.
 - Made the Kd and Kv arguments to calculate_CVMIX_conv() mandatory.
 - Removed the unused halo argument to adjust_salt().
 - Removed the unused Kddt_convect argument to full_convection().
 - Made the halo arguments to full_convection()and smoothed_dRdT_dRdS()
   mandatory.
 - Made the useALEalgorithm argument to geothermal_init() mandatory.
 - Removed the unused initialize_all arguments to Calculate_kappa_shear() and
   Calc_kappa_shear_vertex().
 - Removed the unused I_Ld2_1d and dz_Int_1d arguments to kappa_shear_column().
 - Made 3 arguments to calculate_projected_state() mandatory and reordered the
   arguments accordingly.
 - Eliminating the unused skip_diags arguments to calculateBuoyancyFlux() and
   extractFluxes(), which are now effectively always false.
All answers are bitwise identical, and no output is changed.

  Moved the routine rotate_dyngrid() from the MOM_transcribe_grid module to
rotate_dyn_horgrid() in the MOM_dyn_horgrid module so that this routine can also
be used at some point by SIS2 to implement rotational consistency testing, and
also to reflect that this routine only works with types from its new module.
The two routines are the same apart from some added comments, and the old name
of rotate_dyngrid() is still available from MOM_transcribe_grid via a module use
statement.  All answers are bitwise identical.

  Minimized the dependence on dyn_horgrid in initialize_MOM by working directly
with the horizontal index type whereever possible and by moving the calls that
create the MOM_grid_type earlier in the routine, to limit the duration of the
dyn_horgrid_type, and to better co-locate grid-related parameters in the
parameter_doc files.  Also uses the new interface to rotate_dyn_horgrid from the
MOM_dyn_horgrid module in place of the rotate_dyngrid interface from the
MOM_transcribe_grid module.  All answers are bitwise identical, but the order of
some entries in the MOM_parameter_doc files has changed.

  Modified drivers/unit_drivers/MOM_sum_driver.F90 to compile with the latest
version of the rest of the MOM6 code by using the proper types in the various
initialization calls, and verified that it runs as intended.

* reads in porous topography parameters from CHANNEL_LIST_FILE

*new module to compute curve fit for porous topography

*porous constraints used to modify continuity_PPM, CoriolisAdv, and Rayleigh bottom channel drag

This patch overrides the default clock sync (configured in FMS) for the
CPU clocks inside of the bulk mixed layer's loops.

This prevents model hangs due to an inconsistent number of clock syncs
when different ranks have different size domains.

1. Three typos are corrected.
2. An if-statement for better bound of the Laplacian viscosity at h-cell
is moved outside of the do-loops.

  Corrected the units in comments describing 124 variables in 39 files.  In
addition three unused variables were eliminated.  All answers and output are
bitwise identical.

* Change `hor_visc_CS` pointers to locals

    * equilibrium_value removed from CS and is now local
    * MEKE_CS function arguments to stack

* `mixedlayer_restrat_CS` pointers changed to locals
  MLD_filtered[_slow] pointed moved to allocatables

* MLD argument for `mixedlayer_restrat`

Restore MLD pointer

Passing an uninitialized array is problematic, though passing a pointer
to an uninitialized array is not.

This can be addressed when vertvisc_type is resolved.

* `thickness_diffusion_CSp` is moved to local where possible
* All arrays and most other pointer content is moved to either
  allocatable or local to the type.

* `tidal_forcing_CS` pointers are removed, and its fields are converted
  to allocatables.

  - Note that references are retained in the pressure force and
    barotropic CS instances, to avoid copies.

    Still working through that one...

* Internal tide CS pointer removal (int_tide_CS)
* Diabatic driver's `int_tide_CSp` renamed to `int_tide`

I am unsure if the instance of int_tide_CS in the diabatic driver (where
it is created) needs to be declared as target.  Seems not, but watch
this issue.

This removes just about all of the entrain_diffusive pointers (except
the diag_ctrl).

There is a very minor incongruity with `just_read_params`, which was
originally used to deallocate the CS, which might alter some removed
`if(associated(CS))` checks.  But it seems this is not really a problem,
since the calls to entrainment_diffusion() are inside regions
unreachable when this flag (from `CS%useALEalgorithm`) is true.

* `tidal_mixing_CS` pointers moved to locals
* `tidal_mixing_CSp` in diffusivity renamed to `tidal_mixing`
* Most of the pointer-declared fields converted to allocatables.
* Local `dd` pointers to `CS%dd` removed
* Reorder calculate_tidal_mixing (and sub-procedure) args

* `geothermal_CS` converted from pointers to locals
* Instance of `geothermal_CS` in diabatic driver changed to local

* Diabatic driver `opacity_CSp` renamed to `opacity`, changed to local
* Instances of `optics` and `opacity_CS` converted to locals
* Fields in `opacity_CS` and `optics_type` changed to allocatables

* `bulkmixedlayer_CS` pointers moved to locals

* Diabatic driver renamed variables:
  * `bulkmixedlayer` flag -> `use_bulkmixedlayer`
  * `bulkmixedlayer_CSp` -> `bulkmixedlayer`

* Some redundant documentation removed

* `energetic_PBL_CS` pointers changed to locals in main module
* `energetic_PBL_CSp` changed to local and renamed to `energetic_PBL`
  in diabatic driver.

* `regularize_layer_CS` pointers in module moved to local
* `regularize_layer_CSp` in diabatic driver moved to local
* diabatic drriver `regularize_layer_CSp` renamed to drop `_CSp`

* `CVMix_conv_CS` in diabatic driver renamed to `CVMix_conv`
* Pointer instances of `CVMix_conv_CS` changed to locals
* `CVMix_end` function removed, since it did nothing.

* `MEKE_type` pointers of many arguments and control structures changed
  from pointers to locals

* `MEKE` input removed from the following:
    * `initialize_dyn_unsplit`
    * `initialize_dyn_unsplit_RK2`

* Many `associated(MEKE)` checks have been removed, and now rely on
  associations of individual components within MEKE

  This is just "passing the buck" and not solving the underlying issue
  of decision-by-allocation, but it's closer to a true solution.

* Pointer fields inside `MEKE_type` converted to allocatables

  `associated()` tests for them replaced with `allocatable()`

* `VarMix_CS` pointer instances redefined as locals

* `associated(VarMix)` tests replaced with `VarMix%use_variable_mixing`.

  This ought to be identical, since `VarMix_init()` deallocates the CS
  if this flag is unset (False), and the function is always called.

* VarMix arrays changed from pointers to allocatables

* `wave_speed_CS` pointers redefined as locals
* `wave_speed_CSp` in varmix and diagnostics renamed to `wave_speed`
* `S` and `T` pointers removed

wave speed update

* Most `MOM_restart_CS` instances changed from pointers to locals

* `MOM_restart_CS` removed from unsplit dyncore subroutines

* `restart_CSp` renamed to `restart_CS` in many functions

* Instances of `barotropic_CS` pointers changed to locals
* `barotropic_CSp` removed from MOM module, as it was unused
* `frhat[uv]1` converted to allocatable
* `BT_OBC` field pointers to allocatable

* `wave_structure_CS` instances changed from pointer to local
* T and S aliases to `tv` in `MOM_wave_structure` removed
* `wave_structure_CSp` renamed to `wave_struct` in internal tides

* Some instances of `ALE_sponge_CS` declared as local
* Redfined many allocatable arrays declared as pointers

Much of this module was left unmodified, due to a lot of decision making
based on the associated status of the CS.

* diagnostic field pointers changed to allocatables
* `safe_alloc_ptr` calls replaced with `allocate()`
* Some instances of `diagnostics_CS` passed as type
* `diagnostics_CS` in MOM_mod moved to stack

Convert `set_visc_CS` pointer instances to locals

* `EOS_type` pointers in MOM_EOS_mod moved to locals
* Various `EOS_type` pointers changed to local
* `eqn_of_state` removed from the following:
  - `adjustment_initialize_temperature_salinity`
  - `BFB_set_coord`
  - `dense_water_initialize_TS`
  - `DOME2d_initialize_temperature_salinity`
  - `dumbbell_initialize_temperature_salinity`
  - `Neverworld_initialize_thickness`
  - `Rossby_front_initialize_temperature_salinity`
  - `seamount_initialize_temperature_salinity`
  - `sloshing_initialize_temperature_salinity`
  - `USER_initialize_temperature_salinity`
  - `USER_set_coord`
* `EOS` removed from neutral diffusion unit test

NOTE: eqn_of_state in MOM_mod is retained, since there are many checks
of pointer associated of `tv%eqn_of_state`.

Redefine Coriolis advection pointers as locals

* The following control structures were moved to locals:
  * `PressureForce_CS`
  * `PressureForce_FV_CS`
  * `PressureForce_Mont_CS`
* The `*_end()` functions no longer do anything and were removed

These pointers were defined as locals

* `MOM_continuity_CS`
* `MOM_continuity_PPM_CS`

This patch replaces many pointers in the OBC with local or allocatable
variables.

Notes:
* `OBC` redeclared as `target` in some places for `segment` pointers
* `field_names` removed from `OBC_segment_type`
* `Tr_Reg` removed from `set_tracer_data`
* `OBC` removed from `deallocate_OBC_segment_data`

* Style Fixes

* Store depths for porous curve fitting as [Z ~> m] and account for Z_ref

Correct a couple of typos in hor_visc

  Added a new variable, initialized, to the control structures of modules that
had been testing for an allocated control structure to verify that it had been
initialized before it was going to be used, and then duplicated the tests using
this new variable.  This was done to enable us to go ahead with MOM6 PR #5,
which eliminated many of these checks when converting the control structures
from pointers in the parent modules to elements that are always there, and then
passing them as simple types instead of as pointers.  If we decide that we do
not need these tests after all, we can easily delete them, but until this is
discussed, this commit avoids losing the messages, as it was easier to do it
this way instead of trying to recreate them after they had been removed.  All
answers and output are bitwise identical.

Redefine ~500 pointers as local or stack variables

  Corrected the units or made other clarifications in comments describing 60
variables in 28 files.  In addition three unused (and unscaled) variables were
eliminated.  All answers and output are bitwise identical.

  Add a dimensionally rescaled variable with the radius of the Earth in [L ~> m]
to the ocean_grid_type and dyn_hor_grid type to expand dimensional consistency
testing.  For now it exists along-side the previous variable with the radius of
the Earth in [m], which might be used in other drivers or user code that we are
not aware of.  All instances in the MOM6 code that were using the unscaled
variable G%Rad_Earth were changed to use the dimensionally scaled variable
G%Rad_Earth_L.  In addition, the code for setting up the grid metrics was
simplfied by completing the dimensional rescaling of its internal variables
and some grid rescaling factors that were no longer in use were eliminated.
As a part of this change, a unit_scale_type argument was added to the interface
for USER_initialize_tracer.

  In addition, a number of comments were changed to clearly distinguish between
dimensionally scaled variables that scale back to a nondimensional variable that
can take on a range of values (using the syntax [... ~> nondim]), as opposed to
variables that are only a combination of dimensional scaling factors that
resolve back to 1 in MKS units (using the syntax [... ~> 1]).

  All answers are bitwise identical, but there is one minor interface change
and there are new elements in several widely used transparent types.

* changed porous topo code to preserve dimensions

* readded rotations that got lost in merge

Add initialization tests using CS%initialized

Corrected the descriptions of 60 variables

+Add G%Rad_Earth_L and related code simplification

  Corrected the dimensional rescaling of the explicit bottom stresses that are
passed to btstep() when SPLIT_BOTTOM_STRESS = True.  Without this correction,
solutions would not pass the dimensional consistency tests in this case.
Thankfully, the parameter setting in question does not seem to be widely used,
and even if it is, answers will not change when Z_RESCALE_POWER = 0.  All
answers and output in the MOM6-examples test suite are bitwise identical.

  Refactored the pseudo_salt_tracer code to avoid using fluxes%netSalt, instead
calculating the surface fluxes directly from fluxes%saltFlux, in preparation to
get rid of the largely redundant fluxes%netSalt element, but also to correct for
the fact that fluxes%netSalt does not have proper scaling to pass dimensional
consistency testing.  Also made the CS%diff element of pseudo_salt_tracer_CS
into an allocatable instead of it being a pointer, and changed the tests for
whether it is allocated appropriately.  Several unused variables were
eliminated, and some comments corrected or reformated.  This does not impact
solutions, but the pseudo_salt and pseudo_salt_diff diagnostics are now
invariant to dimensional rescaling, whereas before they were not.  All solutions
and output in MOM6-examples are bitwise identical.

  Eliminated the no-longer used and previously improperly rescaled netSalt
element from the forcing type.  Also added the missing deallocate statements
for fluxes%netMassOut and fluxes%netMassIn in deallocate_forcing_type().  All
answers and output are bitwise identical, although an element has been removed
from a transparent type.